Fig. 3: Human Reference Atlas usage.

a, HRA can be used to compare the distribution of parenchymal cells including endothelial, epithelial and muscle that compose the blood vessels, airways and gas exchanging functional lung structures and resident immune cells including macrophages, to local vasculature (VCCF visualization) in healthy (top) and diseased (bottom) lung using multiplexed immunofluorescence microscopy images with bronchiole (br) and an accompanying small pulmonary artery (pa). Scale bars, white 5 mm; red 200 µm; and yellow 100 µm. The graphs on the right show distance distributions for cell types present in the healthy lung (top) and diseased BPD lung (bottom); the violin plot (middle) shows a comparison between distance distributions for cell types common in both datasets. Datasets are on GitHub⁸¹. b, Multilevel cell neighborhoods can be computed to analyze and communicate the structure and function of FTUs; tissue image with cell type annotations and zoom into H&E with FTU segmentations (red outlines) and zoom into the multiplexed image (CODEX) is shown in left, neighborhoods are given in the middle; hierarchy of FTUs, neighborhoods, communities and cell types are shown on the right. Datasets are on GitHub⁸¹. ICC, Interstitial cells of Cajal; TA, transit-amplifying; NK, natural killer; DC, dendritic cell; IEL, intraepithelial lymphocytes.